running hybrid version

[chris blair]

Hi all, 

I am trying to run raxml on our cluster and am receiving the following error:

PBS: exec of shell '/bin/' failed

Not sure what's going on or what /bin/ is referring to. I am running the script in the same directory as the raxml executable. If I simply type ./raxmlHPC-HYBRID-SSE3 the program loads fine. I am attaching the pbs script in case there is something wrong. Also, any recommendations for setting the parallelization would be welcome. I am still a bit confused about selecting the correct number of MPI processes and threads. Each node of our cluster has 16 cores. 

Chris

[chris blair]

I thought about running raxml-ng instead, but I am having difficulty installing the software on the cluster (see attached). 

[Alexey Kozlov]

Hi Chris,

> I am trying to run raxml on our cluster and am receiving the following error:
>
> PBS: exec of shell '/bin/' failed
>
> Not sure what's going on or what /bin/ is referring to. I am running the script in the same directory as the raxml
> executable. If I simply type ./raxmlHPC-HYBRID-SSE3 the program loads fine. I am attaching the pbs script in case there
> is something wrong.

Please try changing "-# 100" to "-N 100" in RAxML command line.

>Also, any recommendations for setting the parallelization would be welcome. I am still a bit
> confused about selecting the correct number of MPI processes and threads. Each node of our cluster has 16 cores.

This question has been discussed multiple time on this group. If your alignment is large enough, just use 1 thread per
core (-T 16) and 1 MPI rank per node. Otherwise, use 1 thread per ~1000 alignment patterns, and increase the number of
MPI ranks accordingly.

Best,
Alexey

>
> Chris
>
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[Alexey Kozlov]

i can see at least 2 problems in your screen log:

- your system assembler (as) is too old (>= 2.25 required)
- your autoconf is too old (>= 2.64 required)

both can be fixed by loading the respective modules (if available) or asking your admins to install/update them (if not)

[chris blair]

Hi Alexey, 

Changing the # to a N did not fix the error (/bin/failed) with RAxML unfortunately. 

Regarding raxml-ng, I contacted our sys admin and he says the system has autoconf 2.68 installed, but is called autoconf268. Is there a file that I will need to edit to compile successfully?

Chris

[Alexey Kozlov]

Hi Chris,

> Changing the # to a N did not fix the error (/bin/failed) with RAxML unfortunately.

OK, is this error actually RAxML-specific? What if you comment out the line with the RAxML call, will this error disappear?

> Regarding raxml-ng, I contacted our sys admin and he says the system has autoconf 2.68 installed, but is called
> autoconf268. Is there a file that I will need to edit to compile successfully?

Please see here for several methods how to achieve this:

https://unix.stackexchange.com/questions/127888/select-default-binary-to-use


Best,
Alexey

> <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

[chris blair]

Hi Alexey, 

I created an alias to autoconf 2.68 in my ~/.bashrc and called it autoconf. If I type autoconf --version it gives me 2.68. However, when I go to compile it still gives me the same error stating that version 2.64 or higher is required. I'm guessing this might be a system issue?

Chris

[Alexey Kozlov]

sorry there are multiple executables which are part of autoconf/automake package, so you should better use the first
method, i.e. prepend your PATH with the directory where autoconf 2.68 is installed:

https://unix.stackexchange.com/a/127890

[chris blair]

Hi Alexey, 

I added the PATH to my .bashrc (see attached). Unfortunately the issue persists. The software will always try to build with the older version of autoconf (I am guessing because it is called autoconf and not autoconf268). I realize that this is more of a question for our cluster admin. Perhaps it will be best if he simply removes the older version and renames autoconf268 to autoconf.

Chris

[Alexey Kozlov]

yes, please let him help you with this!

Best,
Alexey

On 22.01.2018 15:41, chris blair wrote:
> Hi Alexey,
>

> I added the PATH to my .bashrc (see attached). Unfortunately the issue persists. The software will always try to build
> with the older version of autoconf (I am guessing because it is called autoconf and not autoconf268). I realize that
> this is more of a question for our cluster admin. Perhaps it will be best if he simply removes the older version and
> renames autoconf268 to autoconf.
>
> Chris
>
> On Monday, 22 January 2018 09:00:12 UTC-5, Alexey Kozlov wrote:
>
> sorry there are multiple executables which are part of autoconf/automake package, so you should better use the first
> method, i.e. prepend your PATH with the directory where autoconf 2.68 is installed:
>

> https://unix.stackexchange.com/a/127890 <https://unix.stackexchange.com/a/127890>

[chris blair]

So apparently I can no longer run RAxML from anywhere in my system. I always get the PBS: exec of shell '/bin/' failed error. This is odd because scripts that ran previously are no longer working. I tried downloading and compiling raxml again, but it didn't help. Lol all I want is to be able to run either RAxML or raxml-ng........sigh

Chris

[chris blair]

Hi Alexey, 

So our cluster admin changed it so that autoconf 2.68 is called by default with the autoconf command (see attached). However, for some reason raxml-ng is still saying that version 2.64 or higher is required. Unfortunately our sys admin is at a loss at this point. Perhaps there is more going on here in addition to the autoconf issue? He actually thinks that I will have to go in and modify the source code, but this seems a bit extreme in my opinion and I am obviously hesitant as I am not a programmer. 

Chris 

[Alexey Kozlov]

Hi Chris,

first of all, I'd strongly recommend you/your admin to upgrade your OS since both compilation problems are caused by
(extremely) old versions of system software.

Have you tried to build raxml-ng from a release package with pre-compiled libpll?

https://github.com/amkozlov/raxml-ng/releases/download/0.5.1/raxml-ng_v0.5.1b_linux_x86_64_MPI.zip

Alternatively, you can try to

1) modify line 76 in

raxml-ng/libs/pll-modules/configure.ac

as follows:

AX_EXT

to

#AX_EXT

and 2) modify line 28

raxml-ng/libs/pll-modules/install-with-libpll.sh

and change

./configure $PREFIX_ARG $PLL_ARGS

to

./configure $PREFIX_ARG $PLL_ARGS --disable-avx2


Hope this helps,
Alexey

[chris blair]

Hi Alexey, 

That version was able to compile successfully. 

Chris